Congenital tufting enteropathy is characterized by intractable watery diarrhea, weight loss, malnutrition and growth retardation in newborn. It is a rare autosomal recessive disorder which is caused by mutations in the gene encoding human epithelial cell adhesion molecule (EpCAM). The diagnosis is based on a combination of clinical signs, histological findings and genetic tests that identify a mutation in the EPCAM gene. We report a Turkish neonate with congenital tufting enteropathy presenting to the emergency department with severe watery diarrhea and weight loss. He was diagnosed as having congenital tufting enteropathy based on his clinical signs and genetic analysis. He was fed by total parenteral nutrition and carbohydrate-poor formula. Despite fact that it is often difficult to find the etiology of conditions that cause congenital diarrhea, clinical suspicion and genetic analysis might be helpful in making the diagnosis of congenital tufting enteropathy.